PhD thesis Gijs Selten - Supplementary data

This repository contains the Supplementary data of the experimental chapters published in the PhD thesis of Gijs Selten MSc. Chapter 2 - Functional capacities drive recruitment of bacteria into plant root (already online on bioRxiv --> https://www.biorxiv.org/content/10.1101/2024.08.22.609090v1.article-info) Supplementary data Supplementary tables Chapter 3 - Key genetic components for bacterial success in complex communities revealed using comparative metagenome analysis Supplementary data Orthogroup profiles of SynCom members Figures S7 and S9 (close-up) Chapter 4 - SyFi: generating and using sequence fingerprints to distinguish SynCom isolates SyFi bash script Supplementary data: Microbiome tables - SyFi (minscorefraction 65, 75, 85, 95 (original), and 100%), Salmon directly on amplicons, Qiime2-VSEARCH (95, 97, 98, 99, 100% match), shotgun metagenomics table Percentages mapped reads 16S copy number VSEARCH clustering results 16S fingerprints 16S V3V4 fingerprints 16S V5V7 fingerprints 16S original sequences 16S V3V4 original sequences 16S V5V7 original sequences Chapter 5 - Bacillus: driver of distinct functional states in plant root bacterial synthetic communities Supplementary data Supplementary tables Jaccard Distance matrix on isolate composition Jaccard Distance matrix on genus composition Jaccard Distance matrix on KO composition Bray Curtis Distance matrix on isolate composition Bray Curtis Distance matrix on genus composition Bray Curtis Distance matrix on KO composition